CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY (Unaudited) - USD ($) shares in Thousands, $ in Thousands	Common Stock [Member]	Additional Paid In Capital [Member]	Accumulated Other Comprehensive Loss [Member]	Accumulated Deficit [Member]	Total Ionis Stockholders' Equity [Member]	Noncontrolling Interest in Akcea Therapeutics, Inc. [Member]	Total
Balance at Dec. 31, 2017	$ 125	$ 1,553,681	$ (31,759)	$ (1,241,034)	$ 281,013	$ 84,267	$ 365,280
Balance (in shares) at Dec. 31, 2017	124,976
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 0	0	0	(41,775)	(41,775)	0	(41,775)
Change in unrealized gains (losses), net of tax	0	0	(967)	0	(967)	0	(967)
Foreign currency translation	0	0	92	0	92	0	92
Biogen stock purchase	$ 11	447,954	0	0	447,965	0	447,965
Biogen stock purchase (in shares)	11,502
Issuance of common stock in connection with employee stock plans	$ 1	8,575	0	0	8,576	0	8,576
Issuance of common stock in connection with employee stock plans (in shares)	679
Stock-based compensation expense	$ 0	62,327	0	0	62,327	0	62,327
Noncontrolling interest in Akcea Therapetuics, Inc.	0	(60,976)	0	0	(60,976)	36,914	(24,062)
Balance at Jun. 30, 2018	$ 137	2,011,561	(32,634)	(1,282,809)	696,255	121,181	817,436
Balance (in shares) at Jun. 30, 2018	137,157
Balance at Mar. 31, 2018	$ 125	1,576,954	(33,234)	(1,242,454)	301,391	85,710	387,101
Balance (in shares) at Mar. 31, 2018	125,449
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 0	0	0	(40,355)	(40,355)	0	(40,355)
Change in unrealized gains (losses), net of tax	0	0	563	0	563	0	563
Foreign currency translation	0	0	37	0	37	0	37
Biogen stock purchase	$ 11	447,954	0	0	447,965	0	447,965
Biogen stock purchase (in shares)	11,502
Issuance of common stock in connection with employee stock plans	$ 1	2,911	0	0	2,912	0	2,912
Issuance of common stock in connection with employee stock plans (in shares)	206
Stock-based compensation expense	$ 0	33,876	0	0	33,876	0	33,876
Noncontrolling interest in Akcea Therapetuics, Inc.	0	(50,134)	0	0	(50,134)	35,471	(14,663)
Balance at Jun. 30, 2018	$ 137	2,011,561	(32,634)	(1,282,809)	696,255	121,181	817,436
Balance (in shares) at Jun. 30, 2018	137,157
Balance at Dec. 31, 2018	$ 138	2,047,250	(32,016)	(967,293)	1,048,079	139,081	1,187,160
Balance (in shares) at Dec. 31, 2018	137,929
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 0	0	0	83,567	83,567	0	83,567
Change in unrealized gains (losses), net of tax	0	0	7,775	0	7,775	0	7,775
Foreign currency translation	0	0	(11)	0	(11)	0	(11)
Issuance of common stock in connection with employee stock plans	$ 2	102,002	0	0	102,004	0	102,004
Issuance of common stock in connection with employee stock plans (in shares)	2,600
Stock-based compensation expense	$ 0	87,437	0	0	87,437	0	87,437
Payments of tax withholdings related to vesting of share-based awards	$ 0	(8,034)	0	0	(8,034)	0	(8,034)
Payments of tax withholdings related to vesting of share-based awards (in shares)	(136)
Noncontrolling interest in Akcea Therapetuics, Inc.	$ 0	(51,433)	0	0	(51,433)	48,737	(2,696)
Balance at Jun. 30, 2019	$ 140	2,177,222	(24,252)	(883,726)	1,269,384	187,818	1,457,202
Balance (in shares) at Jun. 30, 2019	140,393
Balance at Mar. 31, 2019	$ 140	2,117,969	(27,608)	(882,850)	1,207,651	179,769	1,387,420
Balance (in shares) at Mar. 31, 2019	139,624
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 0	0	0	(876)	(876)	0	(876)
Change in unrealized gains (losses), net of tax	0	0	3,452	0	3,452	0	3,452
Foreign currency translation	0	0	(96)	0	(96)	0	(96)
Issuance of common stock in connection with employee stock plans	$ 0	34,943	0	0	34,943	0	34,943
Issuance of common stock in connection with employee stock plans (in shares)	774
Stock-based compensation expense	$ 0	41,933	0	0	41,933	0	41,933
Payments of tax withholdings related to vesting of share-based awards	$ 0	(438)	0	0	(438)	0	(438)
Payments of tax withholdings related to vesting of share-based awards (in shares)	(5)
Noncontrolling interest in Akcea Therapetuics, Inc.	$ 0	(17,185)	0	0	(17,185)	8,049	(9,136)
Balance at Jun. 30, 2019	$ 140	$ 2,177,222	$ (24,252)	$ (883,726)	$ 1,269,384	$ 187,818	$ 1,457,202
Balance (in shares) at Jun. 30, 2019	140,393